Grandparent inference from genetic data: The potential for parentage-based tagging programs to identify offspring of hatchery strays

Thomas A. Delomas and Matthew R. Campbell

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Abstract

Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent-grandchild trios using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false positive and false negative error rates and showed that genetic panels containing 500 - 700 single nucleotide polymorphisms or 200 - 300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

Please Read: DOI: 10.1002/nafm.10823

Improving abundance estimates of spring‐summer Snake River Chinook Salmon for fisheries management

August 2022 North American Journal of Fisheries Management

DOI: 10.1002/nafm.10823

D. Katharine Coykendall, Thomas A. Delomas, Matthew Belnap, and Matthew R. Campbell

The Columbia River basin is home to a spring-summer Chinook Salmon run that returns to the Snake River drainage of Idaho, Oregon and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River Basin. However, Snake River spring-summer Chinook Salmon have experienced declines in abundance due to over-fishing, habitat degradation, and dams. Several stocks are listed as threatened under the United States Endangered Species Act and supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, Passive Integrated Transponder (PIT) tagged as juveniles and detected at Lower Granite Dam (LGD), to generate adult abundance estimates. In-season, these estimates inform state and tribal harvest shares and ensure broodstock needs are met. Post-season, they provide smolt-to-adult survival and return rates. Since 2012, parentage-based tagging (PBT) has provided an alternative method to estimate stock- and age- specific returns at LGD, since returning hatchery adults sampled at LGD can be assigned to their parents. We compared stock-specific abundance estimates between PIT- and PBT-derived methodologies for return years 2016 - 2019. Across all years, PIT tag estimates accounted for 65% of the PBT-based estimates at LGD across all age groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT-based estimates should aide in-season harvest management and post-season run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.

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https://cdnsciencepub.com/doi/full/10.1139/cjfas-2020-0152

John S. Hargrove, Carlos A. Camacho, William C. Schrader, John H. Powell, Thomas A. Delomas, Jon E. Hess, Shawn R. Narum, and Matthew R. Campbell. Parentage-based tagging improves escapement estimates for ESA-listed adult Chinook salmon and steelhead in the Snake River basin. Canadian Journal of Fisheries and Aquatic Sciences. 78(4): 349-360. https://doi.org/10.1139/cjfas-2020-0152

BPA funded project (2010-031-00). 

Project Leader:  Tom Delomas, thomas.delomas@idfg.idaho.gov. 

Parentage Based Tagging (PBT) was implemented by IDFG (in collaboration with CRITFC) in 2010 to address gaps in RPA action 50 – Fish Population Status and Monitoring.  It was initiated as a proof of concept study to verify the accuracy and utility of this genetic technology for population monitoring.  Following empirical testing and demonstration, managers incorporated PBT for long-term status and trend monitoring of Snake River steelhead and Chinook Salmon stocks This project genotypes approximately 20,000  samples annually to create PBT parental genetic baselines for hatchery steelhead and Chinook salmon in the Snake River basin.  This includes ~1,500 Fall Chinook salmon from the Nez Perce and Lyons Ferry Fish hatcheries. In doing so, it effectively, permanently genetically marks ~12 million smolts, per species, per year. This project works closely with another BPA funded project (CRITFC:  2008-907-00) to ensure that genetic marker sets used in the Columbia River basin are standardized, providing unprecedented genetic tools for managing wild and hatchery stocks in the basin, with Genetic Stock Identification techniques segregating adult wild runs by stock of origin, and Parentage Based Tagging technologies identifying the stock and age of sampled hatchery fish.

Currently this PBT baselines produced by project 2010-031-00 are used annually:

-To monitor genetic diversity, genetic differentiation, and effective population size of all hatchery stocks within the Snake River basin (Steele et al 2014, 2015, 2016).  Importantly, this project, used in conjunction with the GSI project, estimates the degree of genetic divergence between every hatchery stock within the Snake River basin and associated wild stocks.

-To monitor the proportion of unclipped adult hatchery steelhead returning over Lower Granite Dam, thus improving wild escapement estimation.  For example, in SY2015 Powell et al (2017) estimated that 26.7% of the Chinook Salmon crossing Lower Granite Dam on the Snake River basin that had been phenotypically identified as wild, were actually unclipped hatchery fish identified using PBT.  Similarly, for SY2015, 6.0% of the steelhead crossing Lower Granite Dam on the Snake River basin that had been phenotypically identified as wild, were actually unclipped hatchery fish identified using PBT.

-To monitor the harvest of all Snake River hatchery stocks, including ESA-listed B-run hatchery steelhead in the lower Columbia River sport and tribal fisheries, and within Idaho (Warren et al 2016, Byrne et al 2016).

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Hargrove, J. S., McCane, J., Roth, C. J., High, B., & Campbell, M. R. (2021). Mating systems and predictors of relative reproductive success in a Cutthroat Trout subspecies of conservation concern. Ecology and Evolution, 00, 1– 15. https://doi.org/10.1002/ece3.7914

Mating systems and patterns of reproductive success in fishes play an important role in ecology and evolution. While information on the reproductive ecology of many anadromous salmonids (Oncorhynchus spp.) is well detailed, there is less information for nonanadromous species including the Yellowstone Cutthroat Trout (O. clarkii bouvieri), a subspecies of recreational angling importance and conservation concern. Using data from a parentage-based tagging study, we described the genetic mating system of a migratory population of Yellowstone Cutthroat Trout, tested for evidence of sexual selection, and identified predictors of mating and reproductive success. The standardized variance in mating success (i.e., opportunity for sexual selection) was significantly greater for males relative to females, and while the relationship between mating success and reproductive success (i.e., Bateman gradient) was significantly positive for both sexes, a greater proportion of reproductive success was explained by mating success for males (r2 = 0.80) than females (r2 = 0.59). Overall, the population displayed a polygynandrous mating system, whereby both sexes experienced variation in mating success due to multiple mating, and sexual selection was variable across sexes. Tests for evidence of sexual selection indicated the interaction between mating success and total length best-predicted relative reproductive success. We failed to detect a signal of inbreeding avoidance among breeding adults, but the group of parents that produced progeny were on average slightly less related than adults that did not produce progeny. Lastly, we estimated the effective number of breeders (Nb) and effective population size (Ne) and identified while Nb was lower than Ne, both are sufficiently high to suggest Yellowstone Cutthroat Trout in Burns Creek represent a genetically stable and diverse population.

Parentage-Based Tagging: Reviewing the Implementation of a New Tool for an Old Problem

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Parentage-based tagging (PBT), an innovative and large-scale application of genetic parentage assignments, is transforming how fisheries managers determine the age and origin of sampled fish. PBT is an efficient alternative for mass tagging and has been widely implemented in the Pacific Northwest. While still an emerging technology, PBT is being used to provide information to managers in state, federal, and tribal agencies on the harvest, research, and conservation of Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss in this region. We review the development of PBT in the Pacific Northwest focusing on the technical and logistical challenges for implementing a regional PBT program. We also showcase recent results and review management efforts that made use of PBT-derived data.

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Abstract The transboundary (Idaho, USA; and British Columbia, Canada) population of Burbot Lota lota native to the Kootenai River basin once provided a popular sport and commercial fishery and has been culturally significant to the Kootenai Tribe of Idaho for millennia. However, the population has experienced significant declines over the last 30 years, due primarily to habitat loss and alteration caused by water storage and diversion. By the late 1990s, the population was considered functionally extinct, with estimates of fewer than 50 Burbot in the wild and little to no recruitment, prompting an ongoing international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to rebuild the population and support future tribal subsistence harvest and recreational fisheries. Although supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. To monitor genetic diversity and potential inbreeding in the broodstock and to provide parentage-based tagging of supplementation offspring, we developed a set (N = 96) of highly variable single-nucleotide polymorphism (SNP) genetic markers. The subset of 96 SNP markers was developed from a larger suite of 6,517 SNPs that were discovered by using restriction site-associated DNA sequencing. This cost-efficient technology allows for the rapid discovery of thousands of SNP markers in species that have not been extensively studied previously or for which there are little existing DNA sequence data. We demonstrated high accuracy (>99%) of our SNP set for parentage and individual identification through simulated and empirical tests. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track the growth, survival, and movement of released individuals.

June 24, 2013 Eagle Fish Genetics Lab IDFG

Parentage-based tagging (PBT) is an emerging genetic-based fish tagging method that involves genotyping hatchery broodstock. PBT is a passive non-invasive approach to stock identification because the parents, not the offspring, are genetically sampled at spawning, thereby "tagging" the offspring. This method provides the same information as traditional physical tags but also allows for collection of more detailed information that previously was impossible or impractical to gather using traditional tagging methods.

According to the article published today in the Canadian Journal of Fisheries and Aquatic Sciences: "This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of fisheries-based research and management questions."

Genetically tagging hatchery-reared fish using PBT is extremely efficient because genotyping hundreds of broodstock parents results in millions of tagged offspring. When fully implemented, PBT can "tag" 100% of hatchery-origin fish.

"The role of genetic methods in fisheries management has reached a milestone," says Craig Steele, a researcher at the Idaho Department of Fish and Game's Fish Genetics Laboratory in Eagle, Idaho, and lead author of the study. "The main application of this technology is to provide information on the origin and age of hatchery fish. But it can also provide additional information relevant to conservation and management efforts including assessments of genetic diversity, relative reproductive success, and the heritability of different physical or behavioral traits."

Since 2008, a regional sampling effort by collaborating state, tribal, and federal agencies has resulted in the implementation of this genetic tagging approach in hatchery-origin steelhead and spring-summer Chinook in the Snake River Basin. The Idaho Department of Fish and Game (IDFG) and the Columbia River Inter-Tribal Fish Commission (CRITFC) verified the accuracy of this new approach and presented the results of their collaborative study in the Canadian Journal of Fisheries and Aquatic Sciences.

The IDFG is committed to adopting PBT as a tool for fisheries management. Collaborative efforts with CRITFC are now underway to expand genetic sampling outside the Snake River Basin and throughout the Columbia River Basin. Adopting this genetic approach for large-scale fisheries management positions the region among the first to use this cutting-edge technology.

This article is available free on the CJFAS website: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2012-0451

Fish population surveys on the Boise River below Lucky Peak Reservoir though downtown Boise. Surveys are performed every 3 years to monitor trends in the fish community using electrofishing gear. Fish are momentarily stunned, then weighed, measured and released unharmed